The Championship side drop to 21st in the table, above the relegation zone on goal difference as the south coast club's financial woes continue
Portsmouth, who have suffered similar financial difficulty in the recent past, had their application to go into administration approved by the High Court on Friday.
The deduction leaves Michael Appleton's side 21st in the Championship, out of the bottom three on goal difference.
"Portsmouth Football Club have been deducted 10 points in accordance with Football League rules and regulations.
"This sporting sanction has been implemented with immediate effect, following formal confirmation that the club is in administration. Portsmouth have seven days in which to appeal.
"The Football League will now begin dialogue with the administrator aimed at achieving a successful sale of the club and its continuation in league football."
Portsmouth became the second club in a matter of days to go into administration, following Scottish side Rangers earlier in the week.
Rangers were also deducted 10 points, but remain in second place in the Scottish Premier League, behind rivals Celtic.